Microorganisms

10 pages, 577 KiB

Open AccessReview

Opportunities and Limitations of Molecular Methods for Studying Bat-Associated Pathogens

by Silvia Zemanová, Ľuboš Korytár, Jana Tomčová, Marián Prokeš, Monika Drážovská, Łukasz Myczko, Piotr Tryjanowski, Gréta Nusová, Alicja Matysiak and Anna Ondrejková

Microorganisms 2022, 10(9), 1875; https://doi.org/10.3390/microorganisms10091875 - 19 Sep 2022

Cited by 3 | Viewed by 2639

Abstract

Bats have been identified as reservoirs of zoonotic and potentially zoonotic pathogens. Significant progress was made in the field of molecular biology with regard to infectious diseases, especially those that infect more than one species. Molecular methods, sequencing and bioinformatics have recently become [...] Read more.

Bats have been identified as reservoirs of zoonotic and potentially zoonotic pathogens. Significant progress was made in the field of molecular biology with regard to infectious diseases, especially those that infect more than one species. Molecular methods, sequencing and bioinformatics have recently become irreplaceable tools in emerging infectious diseases research and even outbreak prediction. Modern methods in the molecular biology field have shed more light on the unique relationship between bats and viruses. Here we provide readers with a concise summary of the potential and limitations of molecular methods for studying the ecology of bats and bat-related pathogens and microorganisms. Full article

(This article belongs to the Special Issue Pathogen Infection in Wildlife)

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24 pages, 4927 KiB

Open AccessArticle

Antibacterial and Anti-Inflammatory Activities of Thymus vulgaris Essential Oil Nanoemulsion on Acne Vulgaris

by Farah M. Abdelhamed, Nourtan F. Abdeltawab, Marwa T. ElRakaiby, Rehab N. Shamma and Nayera A. Moneib

Microorganisms 2022, 10(9), 1874; https://doi.org/10.3390/microorganisms10091874 - 19 Sep 2022

Cited by 25 | Viewed by 6369

Abstract

Antibiotics are frequently used in acne treatment and their prolonged use has led to an emergence of resistance. This study aimed to investigate the use of natural antimicrobials as an alternative therapy. The antimicrobial and anti-inflammatory activities of five commonly used essential oils [...] Read more.

Antibiotics are frequently used in acne treatment and their prolonged use has led to an emergence of resistance. This study aimed to investigate the use of natural antimicrobials as an alternative therapy. The antimicrobial and anti-inflammatory activities of five commonly used essential oils (EOs) (tea tree, clove, thyme, mentha and basil EOs), and their possible mechanisms of action against Cutibacterium acnes and Staphylococcus epidermidis, were explored. The effect of the most potent EO on membrane permeability was elucidated and its anti-inflammatory action, when formulated as nanoemulsion, was tested in an in vivo acne model. The in vitro studies showed that thyme EO had the most potent antimicrobial and antibiofilm activity, with phenolics and terpenoids as main antimicrobial constituents of EO. Thyme EO affected cell membrane permeability of both bacterial species, evident by the detection of the leakage of intracellular ions and membrane integrity by the leakage of nucleic acids. Morphological alteration in bacterial cells was confirmed by transmission electron microscopy. Thyme EO nanoemulsion led to the suppression of an inflammatory response in acne animal models along with a bacterial load decrease and positive histopathological changes. Collectively, thyme EO nanoemulsion showed potent antimicrobial and anti-inflammatory effects compared to the reference antibiotics, suggesting its effectiveness as a natural alternative in acne treatment. Full article

(This article belongs to the Special Issue Plant Extracts and Antimicrobials)

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10 pages, 1899 KiB

Open AccessArticle

First Report of Autochthonous Canine Leishmaniasis in Hong Kong

by Jeanine Sandy, Anthony Matthews, Yaarit Nachum-Biala and Gad Baneth

Microorganisms 2022, 10(9), 1873; https://doi.org/10.3390/microorganisms10091873 - 19 Sep 2022

Cited by 1 | Viewed by 2158

Abstract

Canine leishmaniasis is a zoonotic disease caused by Leishmania infantum; transmitted by the bite of phlebotomine sand flies. Leishmania infantum amastigotes were identified by cytology from a locally born Hong Kong dog exhibiting nasal, cutaneous, and systemic disease who was part of [...] Read more.

Canine leishmaniasis is a zoonotic disease caused by Leishmania infantum; transmitted by the bite of phlebotomine sand flies. Leishmania infantum amastigotes were identified by cytology from a locally born Hong Kong dog exhibiting nasal, cutaneous, and systemic disease who was part of a kennel of eight dogs. All eight kennel dogs were subsequently tested serologically by enzyme-linked immunosorbent assay (ELISA) and by polymerase chain reaction (PCR) followed by DNA sequencing for L. infantum infection. The local dog was seropositive and blood and splenic tissue were PCR positive for L. infantum whilst the other kennel dogs were negative on serology and PCR. Autochthonous transmission was suspected for the local dog as Hong Kong lacks known vectors of L. infantum. Either vertical transmission from the deceased dam who had previously died with disease suspicious for leishmaniasis or horizontal transmission from a second non-locally born kennel dog who had been diagnosed previously with leishmaniasis was possible. This is the first recorded autochthonous case of canine leishmaniasis in Hong Kong. Leishmaniasis should be considered as a differential for cutaneous or systemic illness in local untraveled dogs in Hong Kong. In addition, as dogs serve as L. infantum reservoirs for human infection attention should be paid to the possibility of leishmaniasis emerging in Hong Kong. Full article

(This article belongs to the Special Issue Vector-Borne Diseases in Temperate and Tropical Regions)

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25 pages, 1917 KiB

Open AccessArticle

Compositional Dynamics of Gastrointestinal Tract Microbiomes Associated with Dietary Transition and Feeding Cessation in Lake Sturgeon Larvae

by Shairah Abdul Razak, Shaley Valentine, Terence Marsh, John Bauman, Norfarhan Mohd-Assaad and Kim T. Scribner

Microorganisms 2022, 10(9), 1872; https://doi.org/10.3390/microorganisms10091872 - 19 Sep 2022

Cited by 4 | Viewed by 2203

Abstract

Compromised nutritional conditions associated with dietary transitions and feeding cessation in the wild and during fish aquaculture operations are common and can impact growth and survival. These effects are especially prevalent during early ontogenetic stages. We quantified phenotypic and GI tract microbial community [...] Read more.

Compromised nutritional conditions associated with dietary transitions and feeding cessation in the wild and during fish aquaculture operations are common and can impact growth and survival. These effects are especially prevalent during early ontogenetic stages. We quantified phenotypic and GI tract microbial community responses with an emphasis on protease-producing bacteria of lake sturgeon (Acipenser fulvescens) larvae, a species of aquacultural and conservational importance. To quantify responses associated with experimental food transition and feeding cessation, we performed a 36-day feeding experiment using two treatments: control and diet transition. However, larvae in the diet transition treatment failed to undergo transition and ceased feeding. Larvae in the diet transition treatment exhibited lower growth (total length and body weight) and survival than control larvae. Treatment had a greater effect than ontogenetic changes on taxonomic composition and diversity of the GI tract microbial community. Proteobacteria dominated the GI tract microbial community of the diet transition larvae whereas Firmicutes dominated the GI tracts of control larvae. Most of the 98 identified protease-producing isolates in both treatments were from genera Pseudomonas and Aeromonas: taxonomic groups that include known fish pathogens. Overall, failing to transition diets affected responses in growth and GI tract microbiome composition and diversity, with the later dysbiosis being an indicator of morbidity and mortality in larval lake sturgeon. Thus, microbiological interrogations can characterize responses to dietary regimes. The results can inform fish culturalists and microbiologists of the importance of dietary practices consistent with the establishment and maintenance of healthy GI tract microbiota and optimal growth during early ontogeny. Full article

(This article belongs to the Special Issue Microbiomes of Aquatic Organisms)

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16 pages, 3635 KiB

Open AccessArticle

Pep27 Mutant Immunization Inhibits Caspase-14 Expression to Alleviate Inflammatory Bowel Disease via Treg Upregulation

by Hamid Iqbal, Gyu-Lee Kim, Ji-Hoon Kim, Prachetash Ghosh, Masaud Shah, Wonsik Lee and Dong-Kwon Rhee

Microorganisms 2022, 10(9), 1871; https://doi.org/10.3390/microorganisms10091871 - 19 Sep 2022

Cited by 2 | Viewed by 2070

Abstract

Inflammatory bowel disease (IBD) is a highly prevalent gut inflammatory disorder. Complicated clinical outcomes prolong the use of conventional therapy and often lead to compromised immunity followed by adverse events and high relapse rates. Thus, a profound medical intervention is required. Previously, intranasal [...] Read more.

Inflammatory bowel disease (IBD) is a highly prevalent gut inflammatory disorder. Complicated clinical outcomes prolong the use of conventional therapy and often lead to compromised immunity followed by adverse events and high relapse rates. Thus, a profound medical intervention is required. Previously, intranasal immunization of pneumococcal pep27 mutant (Δpep27) exhibited long-lasting protection against immune-related disorders. System biology analysis has predicted an inverse correlation between Δpep27 immunization and gastroenteritis. Recently, we established that Δpep27-elicited Tregs repressed Wnt5a expression and enhanced barrier integrity, suggesting the restoration of immunological tolerance. Therefore, we evaluated whether Δpep27 can alleviate IBD. Δpep27 dose-dependent response was analyzed in dextran sulfate sodium-induced mice using transcriptome analysis. Pro- and anti-inflammatory signatures were cross-correlated by quantitative PCR and western blot analyses. To address the hierarchy regulating the activity of caspase-14, an undefined marker in IBD, and regulatory T cells (Tregs), antibody-based neutralization studies were conducted. Fecal microbiome profiles were analyzed by 16S rRNA pyrosequencing. Δpep27 significantly attenuated dextran sulfate sodium-induced oxidative stress parameters, proinflammatory cytokines, caspase-14 expression level, and upregulated tight junction, anti-inflammatory genes IL-10 and TGF-β1 via upregulation of Tregs to restore healthy gut microbiota. Neutralization studies unveiled that ∆pep27 had a remedial effect via Treg upregulation. Caspase-14, being an important mediator in the pathogenesis of IBD, can be an alternate therapeutic target in IBD. ∆pep27-increased Tregs repressed caspase-14 expression and reversed gut microbial dysbiosis, aiding to re-establish immunological tolerance. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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14 pages, 982 KiB

Open AccessArticle

Microbiota Succession of Whole and Filleted European Sea Bass (Dicentrarchus labrax) during Storage under Aerobic and MAP Conditions via 16S rRNA Gene High-Throughput Sequencing Approach

by Faidra Syropoulou, Dimitrios A. Anagnostopoulos, Foteini F. Parlapani, Evangelia Karamani, Anastasios Stamatiou, Kostas Tzokas, George-John E. Nychas and Ioannis S. Boziaris

Microorganisms 2022, 10(9), 1870; https://doi.org/10.3390/microorganisms10091870 - 19 Sep 2022

Cited by 8 | Viewed by 1904

Abstract

In the present work, the profiles of bacterial communities of whole and filleted European sea bass (Dicentrarchus labrax), during several storage temperatures (0, 4, 8 and 12 °C) under aerobic and Modified Atmosphere Packaging (MAP) conditions, were examined via the 16S [...] Read more.

In the present work, the profiles of bacterial communities of whole and filleted European sea bass (Dicentrarchus labrax), during several storage temperatures (0, 4, 8 and 12 °C) under aerobic and Modified Atmosphere Packaging (MAP) conditions, were examined via the 16S rRNA High-Throughput Sequencing (HTS) approach. Sensorial attributes were also assessed to determine products’ shelf-life. Results indicated that shelf-life was strongly dependent on handling, as well as on temperature and atmosphere conditions. HTS revealed the undisputed dominance of Pseudomonas from the very beginning and throughout storage period in the majority of treatments. However, a slightly different microbiota profile was recorded in MAP-stored fillets at the middle stages of storage, which mainly referred to the sporadic appearance of some bacteria (e.g., Carnobacterium, Shewanella, etc.) that followed the dominance of Pseudomonas. It is noticeable that a major difference was observed at the end of shelf-life of MAP-stored fillets at 12 °C, where the dominant microbiota was constituted by the genus Serratia, while the relative abundance of Pseudomonas and Brochothrix was more limited. Furthermore, at the same temperature under aerobic storage of both whole and filleted fish, Pseudomonas almost co-existed with Acinetobacter, while the presence of both Erwinia and Serratia in whole fish was noteworthy. Overall, the present study provides useful information regarding the storage fate and spoilage status of whole and filleted European sea bass, suggesting that different handling and storage conditions influence the shelf-life of sea bass by favoring or delaying the dominance of Specific Spoilage Organisms (SSOs), affecting in parallel to some extent the formation of their consortium that is responsible for products’ sensorial deterioration. Such findings enrich the current knowledge and should be used as a benchmark to develop specific strategies aiming to delay spoilage and thus increase the products’ added value. Full article

(This article belongs to the Section Food Microbiology)

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18 pages, 1295 KiB

Open AccessReview

The Use of Gut Microbial Modulation Strategies as Interventional Strategies for Ageing

by Ruqaiyyah Siddiqui, Mohammad Ridwane Mungroo, Ahmad M. Alharbi, Hasan Alfahemi and Naveed Ahmed Khan

Microorganisms 2022, 10(9), 1869; https://doi.org/10.3390/microorganisms10091869 - 19 Sep 2022

Cited by 9 | Viewed by 5005

Abstract

Gut microbial composition codevelops with the host from birth and is influenced by several factors, including drug use, radiation, psychological stress, dietary changes and physical stress. Importantly, gut microbial dysbiosis has been clearly associated with several diseases, including cancer, rheumatoid arthritis and Clostridium [...] Read more.

Gut microbial composition codevelops with the host from birth and is influenced by several factors, including drug use, radiation, psychological stress, dietary changes and physical stress. Importantly, gut microbial dysbiosis has been clearly associated with several diseases, including cancer, rheumatoid arthritis and Clostridium difficile-associated diarrhoea, and is known to affect human health and performance. Herein, we discuss that a shift in the gut microbiota with age and reversal of age-related modulation of the gut microbiota could be a major contributor to the incidence of numerous age-related diseases or overall human performance. In addition, it is suggested that the gut microbiome of long-lived animals such as reptiles should be investigated for their unique properties and contribution to the potent defense system of these species could be extrapolated for the benefit of human health. A range of techniques can be used to modulate the gut microbiota to have higher abundance of “beneficial” microbes that have been linked with health and longevity. Full article

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22 pages, 2213 KiB

Open AccessReview

Insight into the Relationship between Oral Microbiota and the Inflammatory Bowel Disease

by Yimin Han, Boya Wang, Han Gao, Chengwei He, Rongxuan Hua, Chen Liang, Shuzi Xin, Ying Wang and Jingdong Xu

Microorganisms 2022, 10(9), 1868; https://doi.org/10.3390/microorganisms10091868 - 19 Sep 2022

Cited by 12 | Viewed by 3921

Abstract

Inflammatory bowel disease has been a growing concern of lots of people globally, including both adults and children. As a chronic inflammatory disease of the intestine, even though the etiology of inflammatory bowel disease is still unclear, the available evidence from clinic observations [...] Read more.

Inflammatory bowel disease has been a growing concern of lots of people globally, including both adults and children. As a chronic inflammatory disease of the intestine, even though the etiology of inflammatory bowel disease is still unclear, the available evidence from clinic observations has suggested a close association with microorganisms. The oral microbiota possesses the characteristics of a large number and abundant species, second only to the intestinal microbiota in the human body; as a result, it successfully attracts the attention of researchers. The highly diverse commensal oral microbiota is not only a normal part of the oral cavity but also has a pronounced impact on the pathophysiology of general health. Numerous studies have shown the potential associations between the oral microbiota and inflammatory bowel disease. Inflammatory bowel disease can affect the composition of the oral microbiota and lead to a range of oral pathologies. In turn, there are a variety of oral microorganisms involved in the development and progression of inflammatory bowel disease, including Streptococcus spp., Fusobacterium nucleatum, Porphyromonas gingivalis, Campylobacter concisus, Klebsiella pneumoniae, Saccharibacteria (TM7), and Candida albicans. Based on the above analysis, the purpose of this review is to summarize this relationship of mutual influence and give further insight into the detection of flora as a target for the diagnosis and treatment of inflammatory bowel disease to open up a novel approach in future clinical practice. Full article

(This article belongs to the Section Gut Microbiota)

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11 pages, 5614 KiB

Open AccessArticle

Inhibitory Effect of Thymol on Tympanostomy Tube Biofilms of Methicillin-Resistant Staphylococcus aureus and Ciprofloxacin-Resistant Pseudomonas aeruginosa

by Eu-Ri Jo, Jeonghyun Oh and Sung Il Cho

Microorganisms 2022, 10(9), 1867; https://doi.org/10.3390/microorganisms10091867 - 19 Sep 2022

Cited by 3 | Viewed by 2100

Abstract

The formation of antibiotic-resistant strain biofilms in tympanostomy tubes results in persistent and refractory otorrhea. In the present study, we investigated the in vitro antibiofilm activity of thymol against biofilms formed by methicillin-resistant Staphylococcus aureus (MRSA) and ciprofloxacin-resistant Pseudomonas aeruginosa (CRPA), using live [...] Read more.

The formation of antibiotic-resistant strain biofilms in tympanostomy tubes results in persistent and refractory otorrhea. In the present study, we investigated the in vitro antibiofilm activity of thymol against biofilms formed by methicillin-resistant Staphylococcus aureus (MRSA) and ciprofloxacin-resistant Pseudomonas aeruginosa (CRPA), using live and dead bacterial staining and adhesion, biofilm formation, biofilm eradication, and biofilm hydrolytic activity assays. The antibiofilm activity of thymol against tympanostomy tube biofilms formed by MRSA and CRPA strains was examined using a scanning electron microscope. In response to thymol treatment, we detected significant concentration-dependent reductions in the viability and adhesion of MRSA and CRPA. Exposure to thymol also inhibited the formation of both MRSA and CRPA biofilms. Furthermore, thymol was observed to enhance the eradication of preformed mature biofilms produced by MRSA and CRPA and also promoted a reduction in the rates of MRSA and CRPA hydrolysis. Exposure to thymol eradicated extracellular polysaccharide present in the biofilm matrix produced by MRSA and CRPA. Additionally, thymol was observed to significantly eradicate MRSA and CRPA biofilms that had formed on the surface on tympanostomy tubes. Collectively, our findings indicate that thymol is an effective inhibitor of MRSA and CRPA biofilms, and accordingly has potential utility as a therapeutic agent for the treatment of biofilm-associated refractory post-tympanostomy tube otorrhea resulting from MRSA and CRPA infection. Full article

(This article belongs to the Section Medical Microbiology)

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19 pages, 1069 KiB

Open AccessReview

Characteristics of the Gut Bacterial Composition in People of Different Nationalities and Religions

by Mikhail Syromyatnikov, Ekaterina Nesterova, Maria Gladkikh, Yuliya Smirnova, Mariya Gryaznova and Vasily Popov

Microorganisms 2022, 10(9), 1866; https://doi.org/10.3390/microorganisms10091866 - 18 Sep 2022

Cited by 30 | Viewed by 7456

Abstract

High-throughput sequencing has made it possible to extensively study the human gut microbiota. The links between the human gut microbiome and ethnicity, religion, and race remain rather poorly understood. In this review, data on the relationship between gut microbiota composition and the nationality [...] Read more.

High-throughput sequencing has made it possible to extensively study the human gut microbiota. The links between the human gut microbiome and ethnicity, religion, and race remain rather poorly understood. In this review, data on the relationship between gut microbiota composition and the nationality of people and their religion were generalized. The unique gut microbiome of a healthy European (including Slavic nationality) is characterized by the dominance of the phyla Firmicutes, Bacteroidota, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia. Among the African population, the typical members of the microbiota are Bacteroides and Prevotella. The gut microbiome of Asians is very diverse and rich in members of the genera Prevotella, Bacteroides Lactobacillus, Faecalibacterium, Ruminococcus, Subdoligranulum, Coprococcus, Collinsella, Megasphaera, Bifidobacterium, and Phascolarctobacterium. Among Buddhists and Muslims, the Prevotella enterotype is characteristic of the gut microbiome, while other representatives of religions, including Christians, have the Bacteroides enterotype. Most likely, the gut microbiota of people of different nationalities and religions are influenced by food preferences. The review also considers the influences of pathologies such as obesity, Crohn’s disease, cancer, diabetes, etc., on the bacterial composition of the guts of people of different nationalities. Full article

(This article belongs to the Special Issue Gut Microbioma Structure and Functions in Human Health and Disease 2.0)

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24 pages, 1590 KiB

Open AccessReview

Bovine Immunity and Vitamin D₃: An Emerging Association in Johne’s Disease

by Taylor L. T. Wherry and Judith R. Stabel

Microorganisms 2022, 10(9), 1865; https://doi.org/10.3390/microorganisms10091865 - 18 Sep 2022

Viewed by 2628

Abstract

Mycobacterium avium subspecies paratuberculosis (MAP) is an environmentally hardy pathogen of ruminants that plagues the dairy industry. Hallmark clinical symptoms include granulomatous enteritis, watery diarrhea, and significant loss of body condition. Transition from subclinical to clinical infection is a dynamic process led by [...] Read more.

Mycobacterium avium subspecies paratuberculosis (MAP) is an environmentally hardy pathogen of ruminants that plagues the dairy industry. Hallmark clinical symptoms include granulomatous enteritis, watery diarrhea, and significant loss of body condition. Transition from subclinical to clinical infection is a dynamic process led by MAP which resides in host macrophages. Clinical stage disease is accompanied by dysfunctional immune responses and a reduction in circulating vitamin D₃. The immunomodulatory role of vitamin D₃ in infectious disease has been well established in humans, particularly in Mycobacterium tuberculosis infection. However, significant species differences exist between the immune system of humans and bovines, including effects induced by vitamin D₃. This fact highlights the need for continued study of the relationship between vitamin D₃ and bovine immunity, especially during different stages of paratuberculosis. Full article

(This article belongs to the Special Issue The Microbial Population of the Gastrointestinal Tract of Animals: Impacts on Host Physiology)

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9 pages, 1015 KiB

Open AccessArticle

Crisis Preparedness Exercise on Rift Valley Fever Introduction into Europe under a One Health Approach

by Ombretta Pediconi, Silvia D’Albenzio, Georgia Gkrintzali, Paolo Calistri and Milen Georgiev

Microorganisms 2022, 10(9), 1864; https://doi.org/10.3390/microorganisms10091864 - 18 Sep 2022

Cited by 2 | Viewed by 1954

Abstract

Crisis preparedness training programmes are substantial for the effective management of contingency plans. Rift Valley Fever (RVF) was chosen as the vector transmitted zoonosis for a crisis preparedness exercise co-organised in 2021 by the European Food Safety Authority (EFSA) and the Istituto Zooprofilattico [...] Read more.

Crisis preparedness training programmes are substantial for the effective management of contingency plans. Rift Valley Fever (RVF) was chosen as the vector transmitted zoonosis for a crisis preparedness exercise co-organised in 2021 by the European Food Safety Authority (EFSA) and the Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale” (IZS-Teramo). The online table-top simulation exercise was planned to strengthen the network of Mediterranean countries on rapid risk assessment, risk/crisis management and risk communication during a human/animal health crisis, adopting the ‘One Health’ approach. Italy, Spain, Portugal, France, Greece, Albania, Croatia, Montenegro and Turkey were the beneficiary countries, while European Commission (EC), European Centre for Disease Prevention and Control (ECDC), World Health Organisation (WHO), World Organisation for Animal Health (WOAH) and Food and Agricultural Organisation (FAO) were the designated observers who were actively involved along the entire capacity building process. The simulation exercise was based on a fictional case study in which the zoonotic mosquito-borne disease, not currently present in Europe, was accidentally introduced into the European Union via the accidental transfer of infected vectors from a RVF-endemic country. The training activity was positively assessed by the participants and useful suggestions were given to address further future similar initiatives. Full article

(This article belongs to the Special Issue Rift Valley Fever Virus Infections)

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12 pages, 1876 KiB

Open AccessArticle

A Plasmid Carrying bla_IMP-56 in Pseudomonas aeruginosa Belonging to a Novel Resistance Plasmid Family

by Jessica Gómez-Martínez, Rosa del Carmen Rocha-Gracia, Elena Bello-López, Miguel Angel Cevallos, Miguel Castañeda-Lucio, Alma López-García, Yolanda Sáenz, Guadalupe Jiménez-Flores, Gerardo Cortés-Cortés and Patricia Lozano-Zarain

Microorganisms 2022, 10(9), 1863; https://doi.org/10.3390/microorganisms10091863 - 17 Sep 2022

Cited by 4 | Viewed by 2774

Abstract

bla_IMP and bla_VIM are the most detected plasmid-encoded carbapenemase genes in Pseudomonas aeruginosa. Previous studies have reported plasmid sequences carrying bla_IMP variants, except bla_IMP-56. In this study, we aimed to characterize a plasmid carrying bla_IMP-56 in [...] Read more.

bla_IMP and bla_VIM are the most detected plasmid-encoded carbapenemase genes in Pseudomonas aeruginosa. Previous studies have reported plasmid sequences carrying bla_IMP variants, except bla_IMP-56. In this study, we aimed to characterize a plasmid carrying bla_IMP-56 in a P. aeruginosa strain isolated from a Mexican hospital. The whole genome of P. aeruginosa strain PE52 was sequenced using Illumina Miseq 2 × 150 bp, with 5 million paired-end reads. We characterized a 27 kb plasmid (pPE52IMP) that carried bla_IMP-56. The phylogenetic analysis of RepA in pPE52IMP and 33 P. aeruginosa plasmids carrying resistance genes reported in the GenBank revealed that pPE52IMP and four plasmids (pMATVIM-7, unnamed (FDAARGOS_570), pD5170990, and pMRVIM0713) were in the same clade. These closely related plasmids belonged to the MOB_P11 subfamily and had similar backbones. Another plasmid (p4130-KPC) had a similar backbone to pPE52IMP; however, its RepA was truncated. In these plasmids, the resistance genes bla_KPC-2, bla_VIM variants, aac(6′)-Ib4, bla_OXA variants, and bla_IMP-56 were inserted between phd and resolvase genes. This study describes a new family of plasmids carrying resistance genes, with a similar backbone, the same RepA, and belonging to the MOB_P11 subfamily in P. aeruginosa. In addition, our characterized plasmid harboring bla_IMP-56 (pPE52IMP) belongs to this family. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Genetic Elements in Bacteria)

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9 pages, 421 KiB

Open AccessCommunication

Enteric Bacteria and Parasites with Pathogenic Potential in Individuals of the Colombian Indigenous Tribe Kogui

by Simone Kann, Gustavo Concha, Thomas Köller, Juliane Alker, Ulrich Schotte, Andreas Hahn, Hagen Frickmann and Philipp Warnke

Microorganisms 2022, 10(9), 1862; https://doi.org/10.3390/microorganisms10091862 - 17 Sep 2022

Cited by 5 | Viewed by 1837

Abstract

The Kogui tribe is an indigenous population living in Colombia. The prevalence values of some enteric bacteria, parasites and microsporidia in Kogui stool samples (n = 192) were assessed by real-time polymerase chain reaction (PCR). Thus, genus- or species-specifically recorded positivity rates [...] Read more.

The Kogui tribe is an indigenous population living in Colombia. The prevalence values of some enteric bacteria, parasites and microsporidia in Kogui stool samples (n = 192) were assessed by real-time polymerase chain reaction (PCR). Thus, genus- or species-specifically recorded positivity rates among the Kogui community were assessed. Protozoa were the leading microorganisms in the stool samples of the Kogui, with an average of 1.5 pathogens per sample, followed by bacteria, with 0.6 pathogens per samples and helminths, with 0.3 pathogens per sample. Microsporidia were not detected. Thereby, the majority of detected protozoa comprised species with questionable etiological relevance such as Blastocystis hominis (n = 173) and Dientamoeba fragilis (n = 44), but also a considerable proportion of Giardia duodenalis (n = 71). Cryptosporidium spp., in contrast, was found in a single instance only. The majority of recorded bacteria were Campylobacter spp., with a strikingly high proportion of 50% (n = 96), followed by Shigella spp./enteroinvasive E. coli (EIEC) (n = 14) and Aeromonas spp. (n = 4). The quantitatively most important detected helminths were Ascaris spp. (n = 15), Hymenolepis spp. (n = 14) and Trichuris trichiura (n = 12), followed by Necator americanus (n = 6), Taenia spp. (n = 3) and Strongyloides stercoralis (n = 3) in descending order of abundance. As expected, the Kogui people’s living conditions comprising poverty, lack of access to clean water and simple housing favor a high number of gastrointestinal infections. Preventive approaches are needed to reduce their risk of infection. Full article

(This article belongs to the Special Issue Infectious Diseases: Clinical Diagnosis and Molecular Epidemiology 2.0)

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14 pages, 1797 KiB

Open AccessArticle

Identification and Characterisation of Nontuberculous Mycobacteria in African Buffaloes (Syncerus caffer), South Africa

by Charlene Clarke, Tanya J. Kerr, Robin M. Warren, Léanie Kleynhans, Michele A. Miller and Wynand J. Goosen

Microorganisms 2022, 10(9), 1861; https://doi.org/10.3390/microorganisms10091861 - 17 Sep 2022

Cited by 6 | Viewed by 2661

Abstract

Diagnosis of bovine tuberculosis (bTB) may be confounded by immunological cross-reactivity to Mycobacterium bovis antigens when animals are sensitised by certain nontuberculous mycobacteria (NTMs). Therefore, this study aimed to investigate NTM species diversity in African buffalo (Syncerus caffer) respiratory secretions and [...] Read more.

Diagnosis of bovine tuberculosis (bTB) may be confounded by immunological cross-reactivity to Mycobacterium bovis antigens when animals are sensitised by certain nontuberculous mycobacteria (NTMs). Therefore, this study aimed to investigate NTM species diversity in African buffalo (Syncerus caffer) respiratory secretions and tissue samples, using a combination of novel molecular tools. Oronasal swabs were collected opportunistically from 120 immobilised buffaloes in historically bTB-free herds. In addition, bronchoalveolar lavage fluid (BALF; n = 10) and tissue samples (n = 19) were obtained during post-mortem examination. Mycobacterial species were identified directly from oronasal swab samples using the Xpert MTB/RIF Ultra qPCR (14/120 positive) and GenoType CMdirect (104/120 positive). In addition, all samples underwent mycobacterial culture, and PCRs targeting hsp65 and rpoB were performed. Overall, 55 NTM species were identified in 36 mycobacterial culture-positive swab samples with presence of esat-6 or cfp-10 detected in 20 of 36 isolates. The predominant species were M. avium complex and M. komanii. Nontuberculous mycobacteria were also isolated from 6 of 10 culture-positive BALF and 4 of 19 culture-positive tissue samples. Our findings demonstrate that there is a high diversity of NTMs present in buffaloes, and further investigation should determine their role in confounding bTB diagnosis in this species. Full article

(This article belongs to the Special Issue Pathogen Infection in Wildlife)

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17 pages, 4429 KiB

Open AccessArticle

Susceptibility of Vegetative Cells and Endospores of Bacillus cereus to Rhamnolipid Biosurfactants and Their Potential Application in Dairy

by Paula de Camargo Bertuso, Crisiane Aparecida Marangon and Marcia Nitschke

Microorganisms 2022, 10(9), 1860; https://doi.org/10.3390/microorganisms10091860 - 17 Sep 2022

Cited by 9 | Viewed by 3304

Abstract

Bacillus cereus is a Gram-positive, endospore-forming bacterium well-known as a food pathogen that causes great losses in the food industry, especially in dairy. In this study, rhamnolipid (RL) biosurfactants were evaluated as a bio-based alternative for controlling the growth of vegetative cells and [...] Read more.

Bacillus cereus is a Gram-positive, endospore-forming bacterium well-known as a food pathogen that causes great losses in the food industry, especially in dairy. In this study, rhamnolipid (RL) biosurfactants were evaluated as a bio-based alternative for controlling the growth of vegetative cells and endospores of B. cereus. RLs were tested against 14 B. cereus strains isolated from different types of foodstuffs. The antimicrobial activity against vegetative cells and endospores revealed minimal inhibitory concentration (MIC) values of 0.098 mg/mL for almost all strains tested and minimal bactericidal concentration (MBC) varying between 0.098 and >25 mg/mL. The presence of RLs inhibited endospore germination by more than 99%, reducing by 5.5 log the outgrowth of strain 0426. Scanning and transmission electron microscopy confirmed that exposure to RL causes damage to the structure of endospores. When skim milk was utilized as a food model, RL inhibited the growth of vegetative cells and endospores of B. cereus, showing MBC of 3.13 mg/mL for the vegetative cells of strain 0426. The surfactant also reduced bacterial growth in milk at refrigerator temperature. The results suggest that RLs are promising candidates for the development of novel strategies to control B. cereus in the food industry. Full article

(This article belongs to the Section Microbial Biotechnology)

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19 pages, 1502 KiB

Open AccessArticle

Rhizocarpon geographicum Lichen Discloses a Highly Diversified Microbiota Carrying Antibiotic Resistance and Persistent Organic Pollutant Tolerance

by Alice Miral, Adam Kautsky, Susete Alves-Carvalho, Ludovic Cottret, Anne-Yvonne Guillerm-Erckelboudt, Manon Buguet, Isabelle Rouaud, Sylvain Tranchimand, Sophie Tomasi and Claudia Bartoli

Microorganisms 2022, 10(9), 1859; https://doi.org/10.3390/microorganisms10091859 - 16 Sep 2022

Viewed by 2771

Abstract

As rock inhabitants, lichens are exposed to extreme and fluctuating abiotic conditions associated with poor sources of nutriments. These extreme conditions confer to lichens the unique ability to develop protective mechanisms. Consequently, lichen-associated microbes disclose highly versatile lifestyles and ecological plasticity, enabling them [...] Read more.

As rock inhabitants, lichens are exposed to extreme and fluctuating abiotic conditions associated with poor sources of nutriments. These extreme conditions confer to lichens the unique ability to develop protective mechanisms. Consequently, lichen-associated microbes disclose highly versatile lifestyles and ecological plasticity, enabling them to withstand extreme environments. Because of their ability to grow in poor and extreme habitats, bacteria associated with lichens can tolerate a wide range of pollutants, and they are known to produce antimicrobial compounds. In addition, lichen-associated bacteria have been described to harbor ecological functions crucial for the evolution of the lichen holobiont. Nevertheless, the ecological features of lichen-associated microbes are still underestimated. To explore the untapped ecological diversity of lichen-associated bacteria, we adopted a novel culturomic approach on the crustose lichen Rhizocarpon geographicum. We sampled R. geographicum in French habitats exposed to oil spills, and we combined nine culturing methods with 16S rRNA sequencing to capture the greatest bacterial diversity. A deep functional analysis of the lichen-associated bacterial collection showed the presence of a set of bacterial strains resistant to a wide range of antibiotics and displaying tolerance to Persistent Organic Pollutants (POPs). Our study is a starting point to explore the ecological features of the lichen microbiota. Full article

(This article belongs to the Section Microbial Biotechnology)

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31 pages, 1391 KiB

Open AccessReview

A Systematic Review of the Distribution of Tick-Borne Pathogens in Wild Animals and Their Ticks in the Mediterranean Rim between 2000 and 2021

by Baptiste Defaye, Sara Moutailler, Vanina Pasqualini and Yann Quilichini

Microorganisms 2022, 10(9), 1858; https://doi.org/10.3390/microorganisms10091858 - 16 Sep 2022

Cited by 5 | Viewed by 2770

Abstract

Tick-borne pathogens (TBPs) can be divided into three groups: bacteria, parasites, and viruses. They are transmitted by a wide range of tick species and cause a variety of human, animal, and zoonotic diseases. A total of 148 publications were found on tick-borne pathogens [...] Read more.

Tick-borne pathogens (TBPs) can be divided into three groups: bacteria, parasites, and viruses. They are transmitted by a wide range of tick species and cause a variety of human, animal, and zoonotic diseases. A total of 148 publications were found on tick-borne pathogens in wild animals, reporting on 85 species of pathogens from 35 tick species and 17 wild animal hosts between 2000 and February 2021. The main TBPs reported were of bacterial origin, including Anaplasma spp. and Rickettsia spp. A total of 72.2% of the TBPs came from infected ticks collected from wild animals. The main tick genus positive for TBPs was Ixodes. This genus was mainly reported in Western Europe, which was the focus of most of the publications (66.9%). It was followed by the Hyalomma genus, which was mainly reported in other areas of the Mediterranean Rim. These TBPs and TBP-positive tick genera were reported to have come from a total of 17 wild animal hosts. The main hosts reported were game mammals such as red deer and wild boars, but small vertebrates such as birds and rodents were also found to be infected. Of the 148 publications, 12.8% investigated publications on Mediterranean islands, and 36.8% of all the TBPs were reported in seven tick genera and 11 wild animal hosts there. The main TBP-positive wild animals and tick genera reported on these islands were birds and Hyalomma spp. Despite the small percentage of publications focusing on ticks, they reveal the importance of islands when monitoring TBPs in wild animals. This is especially true for wild birds, which may disseminate their ticks and TBPs along their migration path. Full article

(This article belongs to the Special Issue Vector-Borne Infections in Wildlife)

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10 pages, 812 KiB

Open AccessArticle

Strong Biofilm Formation and Low Cloxacillin Susceptibility in Biofilm-Growing CC398 Staphylococcus aureus Responsible for Bacteremia in French Intensive Care Units, 2021

by Nathalie van der Mee-Marquet, Sandra Dos Santos, Seydina M. Diene, Isabelle Duflot, Laurent Mereghetti, Anne-Sophie Valentin, Patrice François and on behalf of the SPIADI Collaborative Group

Microorganisms 2022, 10(9), 1857; https://doi.org/10.3390/microorganisms10091857 - 16 Sep 2022

Viewed by 2571

Abstract

A prospective 3-month study carried out in 267 ICUs revealed an S. aureus nosocomial bacteremia in one admitted patient out of 110 in adult and pediatric sectors, and in one out of 230 newborns; 242 S. aureus bacteremias occurred during the study, including [...] Read more.

A prospective 3-month study carried out in 267 ICUs revealed an S. aureus nosocomial bacteremia in one admitted patient out of 110 in adult and pediatric sectors, and in one out of 230 newborns; 242 S. aureus bacteremias occurred during the study, including 7.9% MRSA-bacteremias. In one ICU out of ten, the molecular characteristics, antimicrobial susceptibility profiles and biofilm production of the strains responsible for S. aureus bacteremia were studied. Of the 53 strains studied, 9.4% were MRSA and 52.8% were resistant to erythromycin. MLST showed the predominance of CC398 (37.7% of the strains) followed by CC8 (17.0%), CC45 (13.2%) and CC30 (9.4%). The lukF/S genes were absent from our isolates and tst-1 was found in 9.4% of the strains. Under static conditions and without exposure to glucose, biofilm production was rare (9.4% of the strains, without any CC398). The percentage increased to 62.3% for strains grown in broth supplemented with 1% glucose (including 7 out of 9 CC8 and 17 out of the 20 CC398). Further study of the CC398, including whole genome sequencing, revealed (1) highly frequent patient death within seven days after CC398 bacteremia diagnosis (47.4%), (2) 95.0% of the strains producing biofilm when exposed to sub-inhibitory concentrations of cloxacillin, (3) a stronger biofilm production following exposure to cloxacillin than that observed in broth supplemented with glucose only (p < 0.001), (4) a high minimum biofilm eradication concentration of cloxacillin (128 mg/L) indicating a low cloxacillin susceptibility of biofilm-growing CC398, (5) 95.0% of the strains carrying a ϕSa-3 like prophage and its particular evasion cluster (i.e., yielding chp and scin genes), and (6) 30.0% of the strains carrying a ϕMR11-like prophage and yielding a higher ability to produce biofilm. Our results provide evidence that active surveillance is required to avoid spreading of this virulent staphylococcal clone. Full article

(This article belongs to the Section Medical Microbiology)

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26 pages, 1020 KiB

Open AccessReview

Respiratory Tract Infections and Laboratory Diagnostic Methods: A Review with A Focus on Syndromic Panel-Based Assays

by Adriana Calderaro, Mirko Buttrini, Benedetta Farina, Sara Montecchini, Flora De Conto and Carlo Chezzi

Microorganisms 2022, 10(9), 1856; https://doi.org/10.3390/microorganisms10091856 - 16 Sep 2022

Cited by 29 | Viewed by 27230

Abstract

Respiratory tract infections (RTIs) are the focus of developments in public health, given their widespread distribution and the high morbidity and mortality rates reported worldwide. The clinical spectrum ranges from asymptomatic or mild infection to severe or fatal disease. Rapidity is required in [...] Read more.

Respiratory tract infections (RTIs) are the focus of developments in public health, given their widespread distribution and the high morbidity and mortality rates reported worldwide. The clinical spectrum ranges from asymptomatic or mild infection to severe or fatal disease. Rapidity is required in diagnostics to provide adequate and prompt management of patients. The current algorithm for the laboratory diagnosis of RTIs relies on multiple approaches including gold-standard conventional methods, among which the traditional culture is the most used, and innovative ones such as molecular methods, mostly used to detect viruses and atypical bacteria. The implementation of molecular methods with syndromic panels has the potential to be a powerful decision-making tool for patient management despite requiring appropriate use of the test in different patient populations. Their use radically reduces time-to-results and increases the detection of clinically relevant pathogens compared to conventional methods. Moreover, if implemented wisely and interpreted cautiously, syndromic panels can improve antimicrobial use and patient outcomes, and optimize laboratory workflow. In this review, a narrative overview of the main etiological, clinical, and epidemiological features of RTI is reported, focusing on the laboratory diagnosis and the potentialities of syndromic panels. Full article

(This article belongs to the Section Medical Microbiology)

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18 pages, 689 KiB

Open AccessReview

What Is Candida Doing in My Food? A Review and Safety Alert on Its Use as Starter Cultures in Fermented Foods

by Gilberto Vinícius de Melo Pereira, Bruna Leal Maske, Dão Pedro de Carvalho Neto, Susan Grace Karp, Juliano De Dea Lindner, José Guilherme Prado Martin, Bianca de Oliveira Hosken and Carlos Ricardo Soccol

Microorganisms 2022, 10(9), 1855; https://doi.org/10.3390/microorganisms10091855 - 16 Sep 2022

Cited by 18 | Viewed by 5903

Abstract

The use of yeasts as starter cultures was boosted with the emergence of large-scale fermentations in the 20th century. Since then, Saccharomyces cerevisiae has been the most common and widely used microorganism in the food industry. However, Candida species have also been used [...] Read more.

The use of yeasts as starter cultures was boosted with the emergence of large-scale fermentations in the 20th century. Since then, Saccharomyces cerevisiae has been the most common and widely used microorganism in the food industry. However, Candida species have also been used as an adjuvant in cheese production or as starters for coffee, cocoa, vegetable, meat, beer, and wine fermentations. A thorough screening of candidate Candida is sometimes performed to obtain the best performing strains to enhance specific features. Some commonly selected species include C. pulcherrima (teleomorph Metschnikowia pulcherrima) (wine), C. parapsilosis (teleomorph Monilia parapsilosis) (coffee), C. famata (teleomorph Debaryomyces hansenii) (cheese), and C. zeylanoides (teleomorph Kurtzmaniella zeylanoides) and C. norvegensis (teleomorph Pichia norvegensis) (cocoa). These species are associated with the production of key metabolites (food aroma formation) and different enzymes. However, safety-associated selection criteria are often neglected. It is widely known that some Candida species are opportunistic human pathogens, with important clinical relevance. Here, the physiology and metabolism of Candida species are addressed, initially emphasizing their clinical aspects and potential pathogenicity. Then, Candida species used in food fermentations and their functional roles are reported. We recommended that Candida not be used as food cultures if safety assessments are not performed. Some safety features are highlighted to help researchers choose methods and selection criteria. Full article

(This article belongs to the Special Issue Microbial Safety of Fermented Foods, 2nd Edition)

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17 pages, 5167 KiB

Open AccessArticle

Response Surface Methodology (RSM) Mediated Optimization of Medium Components for Mycelial Growth and Metabolites Production of Streptomyces alfalfae XN-04

by Jing Chen, Xingjie Lan, Ruimin Jia, Lifang Hu and Yang Wang

Microorganisms 2022, 10(9), 1854; https://doi.org/10.3390/microorganisms10091854 - 16 Sep 2022

Cited by 16 | Viewed by 2973

Abstract

Streptomyces alfalfae XN-04 has been reported for the production of antifungal metabolites effectively to control Fusarium wilt of cotton, caused by Fusarium oxysporum f. sp. vasinfectum (Fov). In this study, we used integrated statistical experimental design methods to investigate the optimized [...] Read more.

Streptomyces alfalfae XN-04 has been reported for the production of antifungal metabolites effectively to control Fusarium wilt of cotton, caused by Fusarium oxysporum f. sp. vasinfectum (Fov). In this study, we used integrated statistical experimental design methods to investigate the optimized liquid fermentation medium components of XN-04, which can significantly increase the antifungal activity and biomass of XN-04. Seven variables, including soluble starch, KNO₃, soybean cake powder, K₂HPO₄, MgSO₄·7H₂O, CaCO₃ and FeSO₄·7H₂O, were identified as the best ingredients based on one-factor-at-a-time (OFAT) method. The results of Plackett–Burman Design (PBD) showed that soluble starch, soybean cake powder and K₂HPO₄ were the most significant variables among the seven variables. The steepest climbing experiment and response surface methodology (RSM) were performed to determine the interactions among these three variables and fine-tune the concentrations. The optimal compositions of medium were as follows: soluble starch (26.26 g/L), KNO₃ (1.00 g/L), soybean cake powder (23.54 g/L), K₂HPO₄ (0.27 g/L), MgSO₄·7H₂O (0.50 g/L), CaCO₃ (1.00 g/L) and FeSO₄·7H₂O (0.10 g/L). A verification experiment was then carried out under the optimized conditions, and the results revealed the mycelial dry weight of S. alfalfae XN-04 reaching 6.61 g/L. Compared with the initial medium, a 7.47-fold increase in the biomass was achieved using the optimized medium. Moreover, the active ingredient was purified from the methanol extract of S. alfalfae XN-04 mycelium and then identified as roflamycoin (a polyene macrolide antibiotic). The results may provide new insights into the development of S. alfalfae XN-04 fermentation process and the control of the Fusarium wilt of cotton and other plant diseases. Full article

(This article belongs to the Special Issue Advanced Research on Biological Control of Plant Disease or Microbial Interactions)

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13 pages, 641 KiB

Open AccessReview

Copper Requirement and Acquisition by Marine Microalgae

by Liangliang Kong

Microorganisms 2022, 10(9), 1853; https://doi.org/10.3390/microorganisms10091853 - 16 Sep 2022

Cited by 8 | Viewed by 2303

Abstract

Copper is a critical metal nutrient required by marine microalgae but may be toxic when supplied in excess. Maintaining an optimal intracellular Cu content is thus fundamentally necessary for microalgae and relies on cellular regulatory metabolisms and the process of Cu uptake that [...] Read more.

Copper is a critical metal nutrient required by marine microalgae but may be toxic when supplied in excess. Maintaining an optimal intracellular Cu content is thus fundamentally necessary for microalgae and relies on cellular regulatory metabolisms and the process of Cu uptake that buffers the variation in environmental Cu availability. In this article the current progress in understanding the Cu requirements and acquisition mechanisms of marine microalgae is reviewed. Cu requirement by microalgae is primarily determined by the amount of Cu-dependent enzymes involved in cellular metabolisms and can be adjusted by Cu-sparing pathways. Decrease in metabolic Cu quotas caused a decline in the abundance of cuproenzymes and the dependent cellular metabolisms, and an induction of Cu acquisition pathways. Conventional models of Cu uptake describe the dependence of Cu uptake rate on free Cu²⁺ ions or kinetically labile species. A reductive, high-affinity Cu uptake system in marine microalgae is identified which enables cells to directly utilize organically complexed Cu, highlighting the importance of cell surface Cu reduction in the marine Cu cycle. This review provides new insights into Cu uptake models that may update the existing knowledge of Cu availability in the ocean. Full article

(This article belongs to the Special Issue Metals in Microorganisms: From Cellular Mechanisms to Microbial Communities)

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21 pages, 2855 KiB

Open AccessReview

Competing Endogenous RNA (ceRNA) Networks and Splicing Switches in Cervical Cancer: HPV Oncogenesis, Clinical Significance and Therapeutic Opportunities

by Afra Basera, Rodney Hull, Demetra Demetriou, David Owen Bates, Andreas Martin Kaufmann, Zodwa Dlamini and Rahaba Marima

Microorganisms 2022, 10(9), 1852; https://doi.org/10.3390/microorganisms10091852 - 16 Sep 2022

Cited by 9 | Viewed by 3493

Abstract

Cervical cancer (CC) is the primary cause of female cancer fatalities in low-middle-income countries (LMICs). Persistent infections from the human papillomavirus (HPV) can result in cervical cancer. However, numerous different factors influence the development and progression of cervical cancer. Transcriptomic knowledge of the [...] Read more.

Cervical cancer (CC) is the primary cause of female cancer fatalities in low-middle-income countries (LMICs). Persistent infections from the human papillomavirus (HPV) can result in cervical cancer. However, numerous different factors influence the development and progression of cervical cancer. Transcriptomic knowledge of the mechanisms with which HPV causes cervical cancer pathogenesis is growing. Nonetheless, there is an existing gap hindering the development of therapeutic approaches and the improvement of patient outcomes. Alternative splicing allows for the production of numerous RNA transcripts and protein isoforms from a single gene, increasing the transcriptome and protein diversity in eukaryotes. Cancer cells exhibit astounding transcriptome modifications by expressing cancer-specific splicing isoforms. High-risk HPV uses cellular alternative splicing events to produce viral and host splice variants and proteins that drive cancer progression or contribute to distinct cancer hallmarks. Understanding how viruses utilize alternative splicing to drive pathogenesis and tumorigenesis is essential. Although research into the role of miRNAs in tumorigenesis is advancing, the function of other non-coding RNAs, including lncRNA and circRNA, has been understudied. Through their interaction with mRNA, non-coding RNAs form a network of competing endogenous RNAs (ceRNAs), which regulate gene expression and promote cervical cancer development and advancement. The dysregulated expression of non-coding RNAs is an understudied and tangled process that promotes cervical cancer development. This review will present the role of aberrant alternative splicing and immunosuppression events in HPV-mediated cervical tumorigenesis, and ceRNA network regulation in cervical cancer pathogenesis will also be discussed. Furthermore, the therapeutic potential of splicing disruptor drugs in cervical cancer will be deliberated. Full article

(This article belongs to the Special Issue Oncogenic Role of Viruses and Bacteria)

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23 pages, 2027 KiB

Open AccessArticle

Prevalence, Antibiotics Resistance and Plasmid Profiling of Vibrio spp. Isolated from Cultured Shrimp in Peninsular Malaysia

by Wan Omar Haifa-Haryani, Md. Ali Amatul-Samahah, Mohamad Azzam-Sayuti, Yong Kit Chin, Mohd Zamri-Saad, I. Natrah, Mohammad Noor Azmai Amal, Woro Hastuti Satyantini and Md Yasin Ina-Salwany

Microorganisms 2022, 10(9), 1851; https://doi.org/10.3390/microorganisms10091851 - 16 Sep 2022

Cited by 18 | Viewed by 3437

Abstract

Vibrio is the most common bacterium associated with diseases in crustaceans. Outbreaks of vibriosis pose a serious threat to shrimp production. Therefore, antibiotics are commonly used as preventative and therapeutic measures. Unfortunately, improper use of antibiotics leads to antibiotic resistance. Nevertheless, information on [...] Read more.

Vibrio is the most common bacterium associated with diseases in crustaceans. Outbreaks of vibriosis pose a serious threat to shrimp production. Therefore, antibiotics are commonly used as preventative and therapeutic measures. Unfortunately, improper use of antibiotics leads to antibiotic resistance. Nevertheless, information on the occurrence of Vibrio spp. and antibiotic use in shrimp, particularly in Malaysia, is minimal. This study aimed to provide information on the occurrence of Vibrio spp., its status of antibiotic resistance and the plasmid profiles of Vibrio spp. isolated from cultured shrimp in Peninsular Malaysia. Shrimp were sampled from seven farms that were located in different geographical regions of Peninsular Malaysia. According to the observations, 85% of the shrimp were healthy, whereas 15% were unhealthy. Subsequently, 225 presumptive Vibrio isolates were subjected to biochemical tests and molecular detection using the pyrH gene. The isolates were also tested for antibiotic susceptibility against 16 antibiotics and were subjected to plasmid profiling. Eventually, 13 different Vibrio spp. were successfully isolated and characterized using the pyrH gene. They were the following: V. parahaemolyticus (55%), V. communis (9%), V. campbellii (8%), V. owensii (7%), V. rotiferianus (5%), Vibrio spp. (4%), V. alginolyticus (3%), V. brasiliensis (2%), V. natriegens (2%), V. xuii (1%), V. harveyi (1%), V. hepatarius (0.4%) and P. damselae (3%). Antibiotic susceptibility profiles revealed that all isolates were resistant to penicillin G (100%), but susceptible to norfloxacin (96%). Furthermore, 16% of the isolates revealed MAR of less than 0.2, while 84% were greater than 0.2. A total of 125 isolates harbored plasmids with molecular weights between 1.0 and above 10 kb, detected among the resistant isolates. The resistant isolates were mediated by both chromosomal and plasmid factors. These findings support the use of surveillance data on the emerging patterns of antimicrobial-resistance and plasmid profiles of Vibrio spp. in shrimp farms. The findings from this study can be used to develop a better disease management strategy for shrimp farming. Full article

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15 pages, 1127 KiB

Open AccessArticle

Maize Apoplastic Fluid Bacteria Alter Feeding Characteristics of Herbivore (Spodoptera frugiperda) in Maize

by Sellappan Ranjith, Thangavel Kalaiselvi, Muruganagounder Muthusami and Uthandi Sivakumar

Microorganisms 2022, 10(9), 1850; https://doi.org/10.3390/microorganisms10091850 - 16 Sep 2022

Cited by 5 | Viewed by 1976

Abstract

Maize is an important cereal crop which is severely affected by Spodoptera frugiperda. The study aims to identify endophytic bacteria of maize root and leaf apoplastic fluid with bioprotective traits against S. frugiperda and plant growth promoting properties. Among 15 bacterial endophytic [...] Read more.

Maize is an important cereal crop which is severely affected by Spodoptera frugiperda. The study aims to identify endophytic bacteria of maize root and leaf apoplastic fluid with bioprotective traits against S. frugiperda and plant growth promoting properties. Among 15 bacterial endophytic isolates, two strains—namely, RAF5 and LAF5—were selected and identified as Alcaligenes sp. MZ895490 and Bacillus amyloliquefaciens MZ895491, respectively. The bioprotective potential of B. amyloliquefaciens was evaluated through bioassays. In a no-choice bioassay, second instar larvae of S. frugiperda fed on B. amyloliquefaciens treated leaves (B+) recorded comparatively lesser growth (1.10 ± 0.19 mg mg⁻¹ day⁻¹) and consumptive (7.16 ± 3.48 mg mg⁻¹ day⁻¹) rates. In larval dip and choice bioassay, the same trend was observed. In detached leaf experiment, leaf feeding deterrence of S. frugiperda was found to be greater due to inoculation with B. amyloliquefaciens than Alcaligenes sp. The phenolics content of B. amyloliquefaciens inoculated plant was also found to be greater (3.06 ± 0.09 mg gallic acid g⁻¹). However, plant biomass production was more in Alcaligenes sp inoculated treatment. The study thus demonstrates the potential utility of Alcaligenes sp. and B. amyloliquefaciens for improving growth and biotic (S. frugiperda) stress tolerance in maize. Full article

(This article belongs to the Special Issue Endophytes for Managing Biotic and Abiotic Stress in Plants)

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13 pages, 1170 KiB

Open AccessArticle

Selection of Non-Saccharomyces Wine Yeasts for the Production of Leavened Doughs

by Teresa Zotta, Tiziana Di Renzo, Alida Sorrentino, Anna Reale and Floriana Boscaino

Microorganisms 2022, 10(9), 1849; https://doi.org/10.3390/microorganisms10091849 - 15 Sep 2022

Cited by 8 | Viewed by 1955

Abstract

Background: Non-conventional yeasts (NCY) (i.e., non-Saccharomyces) may be used as alternative starters to promote biodiversity and quality of fermented foods and beverages (e.g., wine, beer, bakery products). Methods: A total of 32 wine-associated yeasts (Campania region, Italy) were genetically identified and [...] Read more.

Background: Non-conventional yeasts (NCY) (i.e., non-Saccharomyces) may be used as alternative starters to promote biodiversity and quality of fermented foods and beverages (e.g., wine, beer, bakery products). Methods: A total of 32 wine-associated yeasts (Campania region, Italy) were genetically identified and screened for decarboxylase activity and leavening ability. The best selected strains were used to study the leavening kinetics in model doughs (MDs). A commercial strain of Saccharomyces cerevisiae was used as the control. The volatile organic profiles of the inoculated MDs were analyzed by solid phase microextraction/gas chromatography-mass spectrometry (SPME/GC-MS). Results: Most of strains belonged to the NCY species Hanseniaspora uvarum, Metschnikowia pulcherrima, Pichia kudriavzevii, Torulaspora delbruekii, and Zygotorulaspora florentina, while a few strains were S. cerevisiae. Most strains of H. uvarum lacked decarboxylase activity and showed a high leaving activity after 24 h of incubation that was comparable to the S. cerevisiae strains. The selected H. uvarum strains generated a different flavor profile of the doughs compared to the S. cerevisiae strains. In particular, NCY reduced the fraction of aldehydes that were potentially involved in oxidative phenomena. Conclusions: The use of NCY could be advantageous in the bakery industry, as they can provide greater diversity than S. cerevisiae-based products, and may be useful in reducing and avoiding yeast intolerance. Full article

(This article belongs to the Special Issue Microorganisms and Fermented Foods)

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24 pages, 3041 KiB

Open AccessReview

Advanced Glycation End Products in Health and Disease

by V. Prakash Reddy, Puspa Aryal and Emmanuel K. Darkwah

Microorganisms 2022, 10(9), 1848; https://doi.org/10.3390/microorganisms10091848 - 15 Sep 2022

Cited by 49 | Viewed by 6971

Abstract

Advanced glycation end products (AGEs), formed through the nonenzymatic reaction of reducing sugars with the side-chain amino groups of lysine or arginine of proteins, followed by further glycoxidation reactions under oxidative stress conditions, are involved in the onset and exacerbation of a variety [...] Read more.

Advanced glycation end products (AGEs), formed through the nonenzymatic reaction of reducing sugars with the side-chain amino groups of lysine or arginine of proteins, followed by further glycoxidation reactions under oxidative stress conditions, are involved in the onset and exacerbation of a variety of diseases, including diabetes, atherosclerosis, and Alzheimer’s disease (AD) as well as in the secondary stages of traumatic brain injury (TBI). AGEs, in the form of intra- and interprotein crosslinks, deactivate various enzymes, exacerbating disease progression. The interactions of AGEs with the receptors for the AGEs (RAGE) also result in further downstream inflammatory cascade events. The overexpression of RAGE and the AGE-RAGE interactions are especially involved in cases of Alzheimer’s disease and other neurodegenerative diseases, including TBI and amyotrophic lateral sclerosis (ALS). Maillard reactions are also observed in the gut bacterial species. The protein aggregates found in the bacterial species resemble those of AD and Parkinson’s disease (PD), and AGE inhibitors increase the life span of the bacteria. Dietary AGEs alter the gut microbiota composition and elevate plasma glycosylation, thereby leading to systemic proinflammatory effects and endothelial dysfunction. There is emerging interest in developing AGE inhibitor and AGE breaker compounds to treat AGE-mediated pathologies, including diabetes and neurodegenerative diseases. Gut-microbiota-derived enzymes may also function as AGE-breaker biocatalysts. Thus, AGEs have a prominent role in the pathogenesis of various diseases, and the AGE inhibitor and AGE breaker approach may lead to novel therapeutic candidates. Full article

(This article belongs to the Section Medical Microbiology)

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17 pages, 2905 KiB

Open AccessArticle

Application of Aspergillus niger in Practical Biotechnology of Industrial Recovery of Potato Starch By-Products and Its Flocculation Characteristics

by Liang Zhang, Guangli Cao, He Liu, Zhenting Wu, Dianliang Gong, Xin Ru, Xiujie Gong, Qiuyue Pi and Qian Yang

Microorganisms 2022, 10(9), 1847; https://doi.org/10.3390/microorganisms10091847 - 15 Sep 2022

Cited by 5 | Viewed by 2411

Abstract

This study developed a practical recovery for potato starch by-products by A. niger and applied it on a plant scale to completely solve the pollution problems. Soughing to evaluate the effect of A. niger applied towards the production of by-products recycling and analyze [...] Read more.

This study developed a practical recovery for potato starch by-products by A. niger and applied it on a plant scale to completely solve the pollution problems. Soughing to evaluate the effect of A. niger applied towards the production of by-products recycling and analyze the composition and characteristics of flocculating substances (FS) by A. niger and advance a possible flocculation mechanism for by-product conversion. After fermentation, the chemical oxygen demand (COD) removal rate, and the conversion rates of cellulose, hemicellulose, pectin, and proteins were 58.85%, 40.19%, 53.29%, 50.14%, and 37.09%, respectively. FS was predominantly composed of proteins (45.55%, w/w) and polysaccharides (28.07%, w/w), with two molecular weight distributions of 7.3792 × 10⁶ Da and 1.7741 × 10⁶ Da and temperature sensitivity. Flocculation was mainly through bridging and ionic bonding, furthermore, sweeping effects may occur during sediment. Flocculation was related to by-products conversion. However, due to severe pollution problems and resource waste, and deficiencies of existing recovery technologies, converting potato starch by-products via A. niger liquid fermentation merits significant consideration. Full article

(This article belongs to the Special Issue Microbial Advances in a Sustainable Environment: Biological Waste Treatment and Bioconversion Technology)

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21 pages, 10760 KiB

Open AccessArticle

Genome-Based Exploration of Rhodococcus Species for Plastic-Degrading Genetic Determinants Using Bioinformatic Analysis

by Jessica Zampolli, Alessandro Orro, Daniele Vezzini and Patrizia Di Gennaro

Microorganisms 2022, 10(9), 1846; https://doi.org/10.3390/microorganisms10091846 - 15 Sep 2022

Cited by 18 | Viewed by 3621

Abstract

Plastic polymer waste management is an increasingly prevalent issue. In this paper, Rhodococcus genomes were explored to predict new plastic-degrading enzymes based on recently discovered biodegrading enzymes for diverse plastic polymers. Bioinformatics prediction analyses were conducted using 124 gene products deriving from diverse [...] Read more.

Plastic polymer waste management is an increasingly prevalent issue. In this paper, Rhodococcus genomes were explored to predict new plastic-degrading enzymes based on recently discovered biodegrading enzymes for diverse plastic polymers. Bioinformatics prediction analyses were conducted using 124 gene products deriving from diverse microorganisms retrieved from databases, literature data, omic-approaches, and functional analyses. The whole results showed the plastic-degrading potential of Rhodococcus genus. Among the species with high plastic-degrading potential, R. erythropolis, R. equi, R. opacus, R. qingshengii, R. fascians, and R. rhodochrous appeared to be the most promising for possible plastic removal. A high number of genetic determinants related to polyester biodegradation were obtained from different Rhodococcus species. However, score calculation demonstrated that Rhodococcus species (especially R. pyridinivorans, R. qingshengii, and R. hoagii) likely possess PE-degrading enzymes. The results identified diverse oxidative systems, including multicopper oxidases, alkane monooxygenases, cytochrome P450 hydroxylases, para-nitrobenzylesterase, and carboxylesterase, and they could be promising reference sequences for the biodegradation of plastics with C−C backbone, plastics with heteroatoms in the main chain, and polyesters, respectively. Notably, the results of this study could be further exploited for biotechnological applications in biodegradative processes using diverse Rhodococcus strains and through catalytic reactions. Full article

(This article belongs to the Special Issue Rhodococcus Species, Their Resistance to Stress and Biotechnological Potential)

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Microorganisms, Volume 10, Issue 9 (September 2022) – 189 articles

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